Uses of Class
org.biojava.utils.ParserException

Packages that use ParserException

Package	Description
org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.tagvalue	Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.

Uses of ParserException in org.biojava.bio.annodb

Constructors in org.biojava.bio.annodb that throw ParserException

Constructor and Description
IndexedAnnotationDB(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory) Create a new IndexedAnnotationDB.

Uses of ParserException in org.biojava.bio.program.gff

Methods in org.biojava.bio.program.gff that throw ParserException

Modifier and Type	Method and Description
protected GFFRecord	GFFParser.createRecord(GFFDocumentHandler handler, List aList, String rest, String comment) Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
int	GFFErrorHandler.invalidEnd(String token) The `end' field of the GFF entry was not a valid value.
int	GFFErrorHandler.AbortErrorHandler.invalidEnd(String token)
int	GFFErrorHandler.invalidFrame(String token) The `frame' field of the GFF entry was not a valid value.
int	GFFErrorHandler.AbortErrorHandler.invalidFrame(String token)
double	GFFErrorHandler.invalidScore(String token) The `score' field of the GFF entry was not a valid value.
double	GFFErrorHandler.AbortErrorHandler.invalidScore(String token)
int	GFFErrorHandler.invalidStart(String token) The `start' field of the GFF entry was not a valid value.
int	GFFErrorHandler.AbortErrorHandler.invalidStart(String token)
StrandedFeature.Strand	GFFErrorHandler.invalidStrand(String token) The `strand' field of the GFF entry was not a valid value.
StrandedFeature.Strand	GFFErrorHandler.AbortErrorHandler.invalidStrand(String token)
void	GFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler) Informs handler of each line of gff read from bReader.
void	GFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler, String locator) Informs handler of each line of GFF read from bReader
static GFFEntrySet	GFFTools.readGFF(BufferedReader gffIn) Read all GFF entries from a buffered reader.
static GFFEntrySet	GFFTools.readGFF(BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.
static GFFEntrySet	GFFTools.readGFF(File inFile) Reads a GFFEntrySet from a file with no filtering.
static GFFEntrySet	GFFTools.readGFF(File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.
static GFFEntrySet	GFFTools.readGFF(String fileName) Deprecated. use: readGff(File)
static GFFEntrySet	GFFTools.readGFF(String fileName, GFFRecordFilter recFilt) Deprecated. use: readGff(File,GFFRecordFilter)

Uses of ParserException in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 that throw ParserException

Modifier and Type	Method and Description
protected GFF3Record	GFF3Parser.createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack) Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
void	GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) Informs handler of each line of gff read from bReader.
void	GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) Informs handler of each line of GFF read from bReader

Uses of ParserException in org.biojava.bio.program.indexdb

Methods in org.biojava.bio.program.indexdb that throw ParserException

Modifier and Type	Method and Description
static void	IndexTools.indexEmbl(String name, File location, File[] seqFiles, int alphabetIdentifier) indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
static void	IndexTools.indexFasta(String name, File location, File[] seqFiles, int alphabetIdentifier) indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
static void	IndexTools.indexGenbank(String name, File location, File[] seqFiles, int alphabetIdentifier) indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
static void	IndexTools.indexSwissprot(String name, File location, File[] seqFiles) indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.

Uses of ParserException in org.biojava.bio.program.tagvalue

Methods in org.biojava.bio.program.tagvalue that throw ParserException

Modifier and Type	Method and Description
Object	RegexChanger.change(Object value)
Object	ChangeTable.Changer.change(Object value) Produce a modified value from an old value.
Object	ChangeTable.ChainedChanger.change(Object value)
Object	ChangeTable.change(Object tag, Object value)
void	SimpleTagValueWrapper.endRecord()
void	TagValueListener.endRecord() The current record has ended.
void	Indexer2.endRecord()
void	AbstractWrapper.endRecord()
void	Indexer.endRecord()
void	StateMachine.endRecord()
void	StateMachine.SimpleStateListener.endRecord()
void	SimpleTagValueWrapper.endTag()
void	TagValueListener.endTag() End the current tag.
void	Aggregator.endTag()
void	TagDropper.endTag()
void	RegexFieldFinder.endTag()
void	AbstractWrapper.endTag()
void	TagDelegator.endTag()
void	MultiTagger.endTag()
void	StateMachine.endTag()
void	StateMachine.SimpleStateListener.endTag()
void	StateMachine.ExitNotification.notifyExit()
TagValue	TagValueParser.parse(Object record)
TagValue	RegexParser.parse(Object o)
void	StateMachine.TransitionTable.put(Object tag, StateMachine.Transition transition) set a Transition within this TransitionTable (2-argument form)
boolean	Parser.read(BufferedReader reader, TagValueParser parser, TagValueListener listener)
void	StateMachine.BasicState.setTransition(Object tag, StateMachine.State destination) set a Transition for this State setting notifyOnExit to false.
void	StateMachine.TransitionTable.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit) set a Transition within this TransitionTable (3-argument form)
void	StateMachine.BasicState.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit) set a Transition for this State
List	ChangeTable.Splitter.split(Object value) Produce a list of values from an old value.
void	SimpleTagValueWrapper.startRecord()
void	TagValueListener.startRecord() A new record is about to start.
void	AbstractWrapper.startRecord()
void	StateMachine.startRecord()
void	StateMachine.SimpleStateListener.startRecord()
void	ValueChanger.startTag(Object tag)
void	SimpleTagValueWrapper.startTag(Object tag)
void	TagValueListener.startTag(Object tag) Start a new tag.
void	Aggregator.startTag(Object tag)
void	TagRenamer.startTag(Object tag)
void	TagDropper.startTag(Object tag)
void	RegexFieldFinder.startTag(Object tag)
void	AbstractWrapper.startTag(Object tag)
void	TagDelegator.startTag(Object tag)
void	MultiTagger.startTag(Object tag)
void	StateMachine.startTag(Object tag) TagValueListener interface
void	StateMachine.SimpleStateListener.startTag(Object tag)
void	StateMachine.State.transit(Object tag)
void	StateMachine.BasicState.transit(Object tag) Find the destination State when the specified tag is encountered.
void	ValueChanger.value(TagValueContext ctxt, Object value)
void	SimpleTagValueWrapper.value(TagValueContext ctxt, Object value)
void	TagValueListener.value(TagValueContext ctxt, Object value) A value has been seen.
void	Aggregator.value(TagValueContext ctxt, Object value)
void	TagDropper.value(TagValueContext ctxt, Object value)
void	RegexFieldFinder.value(TagValueContext ctxt, Object val)
void	AbstractWrapper.value(TagValueContext ctxt, Object value)
void	TagDelegator.value(TagValueContext tvc, Object value)
void	MultiTagger.value(TagValueContext ctxt, Object value)
void	StateMachine.value(TagValueContext ctxt, Object value)
void	StateMachine.SimpleStateListener.value(TagValueContext ctxt, Object value)

Uses of ParserException in org.biojava.bio.program.unigene

Methods in org.biojava.bio.program.unigene that throw ParserException

Modifier and Type	Method and Description
static ParserListener	UnigeneTools.buildDataParser(TagValueListener listener) Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
static ParserListener	UnigeneTools.buildLibInfoParser(TagValueListener listener) Generate a tag-value parser for the library info unigene files.